diff test-data/kmerfilter/kmerfilter.log @ 0:1b6d07160736 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmerfilter/kmerfilter.log	Mon Jul 01 10:57:08 2019 -0400
@@ -0,0 +1,22 @@
+Using a kmer size of 16
+Filtering out reads by identifying rare kmers: On.
+  A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read.
+  A read is dropped when it contains 13 or more rare kmers in a row.
+Filtering out reads by identifying abundant kmers: On.
+  Kmer is considered abundant when it occurs 20000 or more times.
+  A read is dropped when it contains 80% or more abundant kmers.
+Normalizing read depth: Off.
+Found 1 input file(s).
+Found 0 paired input file(s).
+Generating kmer distribution...
+Generating kmers from file 1 of 1 [R1_0001.fastq]
+540 unique k-mers recorded.
+Filtering reads by kmer frequency...
+Processing file 1 of 1 [R1_0001.fastq]
+  5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads.
+Outputing details to log: 'stacks_outputs/kmer_filter.log'
+
+5 total sequences;
+  0 rare k-mer reads;
+  0 abundant k-mer reads;
+5 retained reads.